prf::Rg Class Reference
[Measurements]

Radius of gyration of a section of a protein chain. More...

#include <Rg.hh>

Inherits prf::Observable.

Inheritance diagram for prf::Rg:

[legend]List of all members.

Public Member Functions
int	init_obs ()
	All observables must implement one initialize routine.
void	of_chain (int i)
	Limit to chain i. If i is -1, all chains.
void	refresh (int curT)
	Necessary before an observable value is used.
void	rangeEstimate (double &x1, double &x2)
	Estimate a range in which values of this observable are expected.

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Detailed Description

This observable returns the radius of gyration of all non-hydrogen atoms of a given chain or of the whole population. In the case of rg over many chains, it is assumed that EnforceBC has been called, so that all coordinates are within one unit periodic box. Only non-hydrogen atoms are used in the calculation.

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Member Function Documentation

int Rg::init_obs

(

)

[virtual]

Even if it seems that one particular observable might need additional arguments during initialization, it is advantageous to have a uniform syntax for all of them. So, when additional arguments are needed, one should provide them in a separate function called before initialization, and then call init_obs without arguments. The name init_obs instead of a more natural "init" or "initialize" is because an Observable often inherits from other classes which represent its character more fundamentally. So, the names such as "init" are kept free for such base classes.

Reimplemented from prf::Observable.

void Rg::refresh

(

int

curT

)

[virtual]

This is done because complex observables like RMSD are not evaluated at every step. A call to refresh() would make sure that the Observable has its most current value. The optional argument tindx was introduced in version 1.1 when management of histograms was relocated from ObsHandler class to the Observable class. The argument tells the Observable object about a "temperature index" which it can use to put the current data in the appropriate histogram block.

Reimplemented from prf::Observable.

void Rg::rangeEstimate	(	double &	x1,
		double &	x2
	)			[virtual]

The default is between 0 and 1. So, for observables with values always between 0 and 1, you need not over-write this virtual function. Sometimes the observable will have a different fixed range, determined by its definition. Sometimes the range can not be determined perfectly. In such a case, let this function just return something reasonable.

Reimplemented from prf::Observable.

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The documentation for this class was generated from the following files:

• model/Observables/Rg.hh
• model/Observables/Rg.cc

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PROFASI: Protein Folding and Aggregation Simulator, Version 1.1
© (2005-2008) Anders Irbäck and Sandipan Mohanty
Documentation generated on 10 Oct 2008 using Doxygen version 1.5.0